Cell Biology and Disease

• Covalent cleavage of proteins • Occurs during or after protein biosynthesis • Important component of cell signalling • Occurs on AA chain, usually at a terminal • Extends the 21AAs available, adding/removing chemical groups increases diversity, while extending function and stability.

• True stem cells or adult stem cells • Ability to renew and differentiate, potentially into any cell in the human body. • Unclear how it is maintained and modulated, evidence suggests complex cell signalling networks • Differentiate into 1 of 3 types of germ layers: endoderm, mesoderm, ectoderm. • Induced PSC can be created from differentiated cells. • As development progresses, they lose pluripotency.

• Phosphorylation • Glycosylation • Acetylation • Methylation • Disulphide bonds

• Reversibly add/remove phosphate, causes a conformational change in protein. • Activate/deactivate an enzyme. • 1/3 of cellular proteins thought to be phosphorylated at any given time.

• As P has 2 -ve charges, there can be significant conformational change. • Activate enzyme = form a site recognised by other proteins • Deactivate enzyme = can mask a binding site preventing protein-protein interaction.

A carbohydrate is covalently bound to an N or O (functional group) on a protein, via a glycosidic bond

• Help correct folding • Increase protein stability • Cell-cell / cell-environment adhesion • Immune response • Hormone activity • Embryonic development

• 40 disorders • 13 different monosaccharides involved • 8 different amino acids • > 41 different bonds • 16 enzymes

• N-linked • O-linked • Glypiation • C-linked • Phosphoglycosylation

Bond - Glycan binds to the amino group of asparagine. Location - ER Example - Insulin receptor, ECM, regulation

Bond - monosaccharide binds to the hydroxyl group serine or threonine. Location - ER, Golgi, cytosol, and nucleus. Example - collagen, several pathogenic bacteria secretions to form the ECM

Bond - glycan core links a phospholipid and a protein Example - anchors cell surface proteins

Bond - mannose binds to the indole ring of tryptophan. Example - only mammalian cells, ECM

Glycan binds to serine via phosphodiester bond.

• Catalyse the transfer of a phosphate group from a high energy donor molecule to a specific substrate - phosphorylation. • Allow enzymes to be phosphorylated. • 513 characterised, 478 have a homologous catalytic domain, 35 remaining are atypical. • Reaction is essentially unidirectional, taking Pi from ATP and adding to protein, due to large amount of free energy released from P-P bond in ATP.

• Enzymes that catalyse the removal of a phosphate group from a substrate by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl group (dephosphorylation). • Opposite reaction of a kinase • Can be specific or broad range • Broad range controlled by regulatory proteins • Often in a chain- cell signalling

• Addition/removal of an acetyl group, donated by Acetyl CoA. • Can be enzymatic or non-enzymatic, enzymes involve acetylase or deacetylase. • Some proteins are chromosome related and this indicates its importance in gene expression.

N-terminal and lysine acetylation

• Most common co-translational modification in eukaryotes • Synthesis localisation stability • 80-90% of human proteins • Catalysed by a set of enzyme complexes NATs. NATs transfer an acetyl group from Acetyl CoA to a-amino group of the first AA residue of the protein.

• Often acetylation and deacetylation cycle is linked to transcription factors • Activation of gene expression

• Acetylation of histones encourages binding of effector proteins, relaxation of chromatin conformation, and an increase in transcription. • Also in the synthesis, stability, and localisation of other proteins. • But high-level acetylation associated with transcriptional hyperactivity.

• Targeting HDACs (KDAC) in malignant cells and treatment of neurodegenerative disease. • Development of small-molecule inhibitors (HDI).

• Adds a methyl group, usually at lysine or arginine residues. • Methyl donated by S-adenosylmethionine.

• Carbonyl methylation - generally reversible and used to modulate a reaction. • Nitrogen methylation - generally irreversible creating new amino acids. • Arginine methylation - regulation of RNA processing, gene transcription, DNA damage repair, protein translocation, signal transduction. • Lysine methylation - histone function regulation, epigenetic regulation of transcription, lysine methyltransferase.